4RLF

Crystal structure of a benzoate coenzyme A ligase with p-Toluic acid and o-Toluic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V7B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	15 % PEG 3350, 0.1 M Tris pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.716	α = 90
b = 95.366	β = 104.69
c = 95.785	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2011-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97872	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.73	50	95.7	0.09	0.06	17.8	4.8		96640			22.18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.76	72.1		0.654	0.574	1.52	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2V7B	1.73	32.23	96612	5121	95.69	0.16121	0.1594	0.19525	RANDOM	22.318

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.094
r_dihedral_angle_4_deg	18.174
r_dihedral_angle_3_deg	12.403
r_dihedral_angle_1_deg	6.601
r_long_range_B_refined	5.641
r_long_range_B_other	5.562
r_scangle_other	4.351
r_scbond_it	2.96
r_scbond_other	2.96
r_mcangle_it	2.778
r_mcangle_other	2.778
r_mcbond_it	2.056
r_mcbond_other	2.051
r_angle_refined_deg	1.966
r_angle_other_deg	0.952
r_chiral_restr	0.158
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7792
Nucleic Acid Atoms
Solvent Atoms	544
Heterogen Atoms	88

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling